run_metadata: 76480

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
76480	SRR24992467	SRX20748471	SRS18037870	SRP445344	PRJNA986481	Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy	GSE235571	Transcriptome Analysis	X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently there are no approved treatments though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However four patients with XLMTM treated with gene therapy have died from progressive liver failure and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux structural abnormalities of the bile canaliculus and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly we completed a targeted chemical screen and found that Dynasore a dynamin II inhibitor is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings 20 livers per replicate and 3 replicates per genotype by using Arcturus PicoPure RNA isolation kit Applied Biosystems KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.		pubmed:37490339		WT EToH set 1 S14	GSM7505568		source name:liver\|tissue:liver\|genotype:WT\|time:7dpf\|treatment:EToH treated animal\|geo loc name:missing\|collection date:missing	WT EToH set 1 S14	Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate	liver		Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings 20 livers per replicate and 3 replicates per genotype by using Arcturus PicoPure RNA isolation kit Applied Biosystems KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol. The 40 samples were submitted to the Centre for Applied Genomics TCAG Toronto Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.		tissue:liver\|genotype:WT\|time:7dpf\|treatment:EToH treated animal	GSM7505568	GSM7505568: WT EToH set 1 S14; Danio rerio; RNA Seq	GSM7505568 r1	GSM7505568	1	Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings 20 livers per replicate and 3 replicates per genotype by using Arcturus PicoPure RNA isolation kit Applied Biosystems KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. The 40 samples were submitted to the Centre for Applied Genomics TCAG Toronto Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP445344		loader:fastq load.py	WT_EToH_set_1_S14_L001_R2_001.fastq.gz WT_EToH_set_1_S14_L001_R1_001.fastq.gz	fastq fastq	4020460944.0	19903272.0	GSM7505568 r1	0:101 1:101	A:1112138605;C:908652797;G:856383523;T:1143254241;N:31778	101	101			1112138605	908652797	856383523	1143254241	31778	SRX20748471	SRS18037870	SRA1660605	Hospital for Sick Children	GraphiteBio	2	0.91623	0.91517	0.08179	0.08205	0.81866	0.81962	0.65131	0.64895	101	101	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		United States	2023-06-22	Larval	Larval	Liver	Liver and Biliary System